NucPred on Proteomes

Authors: Andrea Krings, Amine Heddad, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred - predictions for eukaryotic proteomes

Species:

Note: All filters/tests are combined with AND unless otherwise stated

Show only the proteins with links to database(s):
OMIM - human disease genes
PDB - protein 3D structure
( AND OR combination )

Annotation filters (can be slow! - Perl regexps allowed: e.g. nucleus|nucleolus)

UniProt ID (e.g. "PK3B_")
UniProt description (e.g. "kinase")
UniProt subcellular location
AND
UniProt GO component
AND
AND the
AND the

Only show proteins where the PredictNLS prediction is:

positive
negative

Only show proteins where the PSORT II predicted location

is is not

Click here: to filter by NucPred score

exclude all transmembrane proteins predicted by TMHMM
don't exclude lone N-terminal predicted transmembrane helices
(these could be signal peptides)

export all ACs and IDs as text file

Show proteins (ordered by NucPred score ) from to (currently 98716 matches)

You can bookmark/save your search criteria with this link. You can also start again with default settings.

UniProt accession	UniProt ID	UniProt description	NucPred score	Predict- NLS	PSORT II	TMHMM #helices	UniProt annotation for subcellular location	Uniprot GO cellular component	OMIM	PDB	sequence length
Q6BX67 UniProt NPD GO	MRS2_DEBHA	Inner membrane magnesium transporter MRS2, mitochondrial precursor (RNA-splicing protein MRS2)	0.34	-	nuc	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				476
Q8BYN3 UniProt NPD GO	ITPK1_MOUSE	Inositol-tetrakisphosphate 1-kinase (EC 2.7.1.134) (Inositol-triphosphate 5/6-kinase) (EC 2.7.1.-) ( ...	0.34	-	cyt	0					419
P51459 UniProt NPD GO	IGF2_HORSE	Insulin-like growth factor II precursor (IGF-II) (Somatomedin A)	0.34	-	exc	0	Secreted protein				181
P09535 UniProt NPD GO	IGF2_MOUSE	Insulin-like growth factor II precursor (Multiplication-stimulating polypeptide) (IGF-II)	0.34	-	exc	1 *	Secreted protein				180
P12843 UniProt NPD GO	IBP2_RAT	Insulin-like growth factor-binding protein 2 precursor (IGFBP-2) (IBP-2) (IGF-binding protein 2) (BR ...	0.34	-	exc	0	Secreted protein	extracellular space [IMP]			304
Q05716 UniProt NPD GO	IBP4_BOVIN	Insulin-like growth factor-binding protein 4 precursor (IGFBP-4) (IBP-4) (IGF-binding protein 4)	0.34	-	exc	0	Secreted protein				258
Q91687 UniProt NPD GO	ITA4_XENLA	Integrin alpha-4 precursor (Integrin alpha-IV) (VLA-4)	0.34	-	nuc	1	Membrane; single-pass type I membrane protein				1032
Q13683 UniProt NPD GO	ITA7_HUMAN	Integrin alpha-7 precursor [Contains: Integrin alpha-7 heavy chain; Integrin alpha-7 light chain]	0.34	+	end	2 *	Membrane; single-pass type I membrane protein		600536		1181
P11215 UniProt NPD GO	ITAM_HUMAN	Integrin alpha-M precursor (Cell surface glycoprotein MAC-1 alpha subunit) (CR-3 alpha chain) (Leuko ...	0.34	-	end	1	Membrane; single-pass type I membrane protein	integrin complex [TAS]	120980	1NA5	1152
P01578 UniProt NPD GO	IFNB1_BOVIN	Interferon beta-1 precursor	0.34	-	mit	0	Secreted protein				186
P07352 UniProt NPD GO	IFNW1_BOVIN	Interferon omega-1 precursor (Interferon alpha-II-1) (IFN-omega-c1)	0.34	-	end	0	Secreted protein				195
Q98925 UniProt NPD GO	IRF2_CHICK	Interferon regulatory factor 2 (IRF-2)	0.34	-	nuc	0	Nucleus				348
O14896 UniProt NPD GO	IRF6_HUMAN	Interferon regulatory factor 6 (IRF-6)	0.34	-	nuc	0	Nucleus (Potential)		608864		467
P56828 UniProt NPD GO	IFNT1_SHEEP	Interferon tau-1 precursor (IFN-tau1) (Trophoblast protein 1) (TP-1) (Trophoblastin) (Antiluteolysin ...	0.34	-	mit	1 *	Secreted protein. Secreted into the uterine lumen			1B5L	195
P28169 UniProt NPD GO	IFNTB_SHEEP	Interferon tau-11 precursor (IFN-tau11) (Trophoblast protein 1) (TP-1) (Trophoblastin) (Antiluteolys ...	0.34	-	mit	1 *	Secreted protein. Secreted into the uterine lumen			1OVI	195
P79182 UniProt NPD GO	IL1B_MACFA	Interleukin-1 beta precursor (IL-1 beta)	0.34	-	cyt	0	Secreted protein. The lack of a specific hydrophobic segment in the precursor sequence suggests that ...				268
Q29053 UniProt NPD GO	IL12A_PIG	Interleukin-12 alpha chain precursor (IL-12A) (Cytotoxic lymphocyte maturation factor 35 kDa subunit ...	0.34	-	exc	0	Secreted protein				222
Q96F46 UniProt NPD GO	I17RA_HUMAN	Interleukin-17 receptor A precursor (IL-17 receptor)	0.34	-	end	2 *	Membrane; single-pass type I membrane protein (By similarity)	integral to plasma membrane [NAS]	605461		866
P01586 UniProt NPD GO	IL3_MOUSE	Interleukin-3 precursor (IL-3) (Multipotential colony-stimulating factor) (Hematopoietic growth fact ...	0.34	-	nuc	1 *	Secreted protein				166
P46652 UniProt NPD GO	IL4_CERTO	Interleukin-4 precursor (IL-4) (B-cell stimulatory factor 1) (BSF-1) (Lymphocyte stimulatory factor ...	0.34	-	exc	0	Secreted protein	extracellular space [ISS]			153
Q00560 UniProt NPD GO	IL6RB_MOUSE	Interleukin-6 receptor beta chain precursor (IL-6R-beta) (Interleukin 6 signal transducer) (Membrane ...	0.34	-	nuc	1	Membrane; single-pass type I membrane protein				917
Q8TAC2 UniProt NPD GO	JOS2_HUMAN	Josephin-2 (Josephin domain-containing protein 2)	0.34	-	cyt	0					188
P02535 UniProt NPD GO	K1C10_MOUSE	Keratin, type I cytoskeletal 10 (Cytokeratin-10) (CK-10) (Keratin-10) (K10) (56 kDa cytokeratin) (Ke ...	0.34	-	mit	0		keratin filament [IDA]			569
P13646 UniProt NPD GO	K1C13_HUMAN	Keratin, type I cytoskeletal 13 (Cytokeratin-13) (CK-13) (Keratin-13) (K13)	0.34	-	cyt	0			193900		458
P60369 UniProt NPD GO	KR103_HUMAN	Keratin-associated protein 10-3 (Keratin-associated protein 10.3) (High sulfur keratin-associated pr ...	0.34	-	nuc	0					221
O35367 UniProt NPD GO	KERA_MOUSE	Keratocan precursor (KTN) (Keratan sulfate proteoglycan keratocan)	0.34	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				351
P09805 UniProt NPD GO	KTXA_KLULA	Killer toxin subunits alpha/beta precursor (RF2 protein) [Contains: Killer toxin subunit alpha; Kill ...	0.34	-	end	3					1146
Q80W68 UniProt NPD GO	KIRR1_MOUSE	Kin of IRRE-like protein 1 precursor (Kin of irregular chiasm-like protein 1) (Nephrin-like protein ...	0.34	-	end	1 *	Membrane; single-pass type I membrane protein (Potential). Predominantly located at podocyte slit di ...				789
Q8NCW0 UniProt NPD GO	KREM2_HUMAN	Kremen protein 2 precursor (Kringle-containing protein marking the eye and the nose) (Kringle domain ...	0.34	-	exc	1	Membrane; single-pass type I membrane protein (Potential)		609899		462
Q9SHE9 UniProt NPD GO	LBD4_ARATH	LOB domain-containing protein 4	0.34	-	nuc	0					172
P09443 UniProt NPD GO	LE19_GOSHI	Late embryogenesis abundant protein D-19 (LEA D-19)	0.34	-	nuc	0					102
P13940 UniProt NPD GO	LEA29_GOSHI	Late embryogenesis abundant protein D-29 (LEA D-29)	0.34	-	exc	0					302
P50595 UniProt NPD GO	LEP_BOVIN	Leptin precursor (Obesity factor)	0.34	-	exc	0	Secreted protein (Probable)				167
P48356 UniProt NPD GO	LEPR_MOUSE	Leptin receptor precursor (LEP-R) (OB receptor) (OB-R) (B219) (CD295 antigen)	0.34	-	end	3 *	Cell membrane; single-pass type I membrane protein. Isoform E: Secreted protein (Probable)	integral to plasma membrane [TAS]			1162
Q5BH52 UniProt NPD GO	LCMT2_EMENI	Leucine carboxyl methyltransferase 2 (EC 2.1.1.-)	0.34	+	nuc	0					1058
Q8N145 UniProt NPD GO	LGI3_HUMAN	Leucine-rich repeat LGI family member 3 precursor (Leucine-rich glioma-inactivated protein 3) (LGI1- ...	0.34	-	end	0	Secreted protein (Potential)		608302		548
Q8K099 UniProt NPD GO	LRC21_MOUSE	Leucine-rich repeat-containing protein 21 precursor (Photoreceptor-associated LRR superfamily protei ...	0.34	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				618
Q8WV35 UniProt NPD GO	LRC29_HUMAN	Leucine-rich repeat-containing protein 29 (F-box/LRR-repeat protein 9) (F-box and leucine-rich repea ...	0.34	-	nuc	0					223
Q8BMT4 UniProt NPD GO	LRC33_MOUSE	Leucine-rich repeat-containing protein 33 precursor	0.34	-	cyt	1	Membrane; single-pass type I membrane protein (Potential)				693
Q09996 UniProt NPD GO	SYLC_CAEEL	Leucyl-tRNA synthetase (EC 6.1.1.4) (Leucine--tRNA ligase) (LeuRS)	0.34	-	cyt	0					1186
Q9MUM1 UniProt NPD GO	CHLN_MESVI	Light-independent protochlorophyllide reductase subunit N (EC 1.18.-.-) (LI-POR subunit N) (DPOR sub ...	0.34	+	cyt	0	Plastid; chloroplast				446
Q85WU5 UniProt NPD GO	CHLN_PINKO	Light-independent protochlorophyllide reductase subunit N (EC 1.18.-.-) (LI-POR subunit N) (DPOR sub ...	0.34	-	cyt	0	Plastid; chloroplast				470
P80471 UniProt NPD GO	LIPC_SOLTU	Light-induced protein, chloroplast precursor (Chloroplastic drought-induced stress protein CDSP-34)	0.34	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane	thylakoid membrane (sensu Viridiplantae) [IEP]			326
Q7ZUA6 UniProt NPD GO	LMBR1_CHICK	Limb region 1 protein homolog	0.34	+	end	9 *	Membrane; multi-pass membrane protein (By similarity)				488
P36776 UniProt NPD GO	LONM_HUMAN	Lon protease homolog, mitochondrial precursor (EC 3.4.21.-) (Lon protease-like protein) (LONP) (LONH ...	0.34	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [TAS]	605490		959
Q9UKU0 UniProt NPD GO	ACSL6_HUMAN	Long-chain-fatty-acid--CoA ligase 6 (EC 6.2.1.3) (Long-chain acyl-CoA synthetase 6) (LACS 6)	0.34	-	nuc	1 *	Mitochondrion; mitochondrial outer membrane; single-pass type III membrane protein (By similarity). ...	microsome [NAS] mitochondrial outer membrane [NAS] peroxisomal membrane [NAS] plasma membrane [NAS]	604443		697
P24666 UniProt NPD GO	PPAC_HUMAN	Low molecular weight phosphotyrosine protein phosphatase (EC 3.1.3.48) (LMW-PTP) (Low molecular weig ...	0.34	-	nuc	0	Cytoplasm	soluble fraction [TAS]	171500	5PNT	157
Q9Y6Y9 UniProt NPD GO	LY96_HUMAN	Lymphocyte antigen 96 precursor (MD-2 protein) (ESOP-1)	0.34	-	exc	0	Secreted protein; extracellular space	plasma membrane [TAS]	605243	1T2Z	160
P58022 UniProt NPD GO	LOXL2_MOUSE	Lysyl oxidase homolog 2 precursor (EC 1.4.3.-) (Lysyl oxidase-like protein 2)	0.34	-	cyt	0	Secreted protein; extracellular space (Potential)				776
Q22099 UniProt NPD GO	SYK_CAEEL	Lysyl-tRNA synthetase (EC 6.1.1.6) (Lysine--tRNA ligase) (LysRS)	0.34	-	nuc	0	Cytoplasm (Potential)				572

You are viewing entries 36801 to 36850 of 98716. You can see more proteins by changing the limits in the form at the top of this page, or click here for the next page of proteins .

If you find NucPred useful, please cite this paper:

NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022

The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold	Specificity	Sensitivity
see above	fraction of proteins predicted to be nuclear that actually are nuclear	fraction of true nuclear proteins that are predicted (coverage)
0.10	0.45	0.88
0.20	0.52	0.83
0.30	0.57	0.77
0.40	0.63	0.69
0.50	0.70	0.62
0.60	0.71	0.53
0.70	0.81	0.44
0.80	0.84	0.32
0.90	0.88	0.21
1.00	1.00	0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

Go back to the NucPred Home Page.